List of Publications of Bhaskar DasGupta

List of Publications of Bhaskar DasGupta

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Publications by year
Not published yet,    2019 and "to appear",    2018,    2017,    2016,    2015,    2014,    2013,    2012,    2011,    2010,    2009,    2008,    2007,    2006,    2005,    2004,    2003,    2002,    2001,    2000,    1999,    1998,    1997,    1996,    1995,    1994,    1993,    1992,    1990,    1989

Not published yet (in preparation, submitted etc.)
2019 and beyond
2018
2017
2016
2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

2003

2002

2001

2000

1999

1998

1997

1996

1995

1994

1993

1992

1990
  • Sudeb Pal, Bhaskar DasGupta and C.E. Veni Madhavan, Optimal Polygon Placement by Translation, 2nd Canadian Conference on Computational Geometry, 164-171, 1990.

1989




Publications by category
Not published yet,    Book,    Editorial foreword to journal special issue,    Journal,    Conference with published proceedings,    Chapter in edited book,    Unpublished but cited technical reports,    Conference without published proceedings   

"Yet uncategorized" (under submission, in preparation etc.)


"Book"

"Editorial foreword to journal special issue" (in reverse chronological order)

"Journal" (in reverse chronological order)
  1. Farzane Yahyanejad, Bhaskar DasGupta and Réka Albert, A survey of some tensor analysis techniques for biological systems, to appear in Quantitative Biology.

  2. Tanima Chatterjee, Bhaskar DasGupta, Nasim Mobasheri, Venkatkumar Srinivasan and Ismael G. Yero, On the Computational Complexities of Three Privacy Measures for Large Networks Under Active Attack, Theoretical Computer Science, 775, 53-67, 2019.
         Here are some pdf slides for these results (from the talk at 25th LSD & LAW).

  3. Bhaskar DasGupta, Nasim Mobasheri and Ismael G. Yero, On analyzing and evaluating privacy measures for social networks under active attack, Information Sciences, 473, 87-100, 2019.

  4. Daniel Ayala, Ouri Wolfson, Bhaskar DasGupta, Jie Lin and Bo Xu, Spatio-temporal Matching for Urban Transportation Applications, ACM Transactions on Spatial Algorithms and Systems, 3(4), 11:1-11:39, 2018.

  5. Bhaskar DasGupta and Nasim Mobasheri, On optimal approximability results for computing the strong metric dimension, Discrete Applied Mathematics, 221, 18-24, 2017.

    Here are some pdf slides for these results (from the talk at the 8th Slovenian International Conference on Graph Theory, Kranjska Gora, Slovenia, 2015).

  6. Bhaskar DasGupta, Marek Karpinski, Nasim Mobasheri and Farzane Yahyanejad, Effect of Gromov-hyperbolicity Parameter on Cuts and Expansions in Graphs and Some Algorithmic Implications, Algorithmica, 80(2), 772-800, 2018.

    Here are some pdf slides for these results (from the talk at BCTCS-2016).

  7. Andreas D.M. Gunawan, Bhaskar DasGupta and Louxin Zhang, A Decomposition Theorem and Two Algorithms for Reticulation-Visible Networks, Information and Computation, 252, 161-175, 2017.

  8. Chun-An Chou, Zhe Liang, Wanpracha Chaovalitwongse, Tanya Y. Berger-Wolf, Bhaskar DasGupta, Saad Sheikh, Mary V. Ashley and Isabel C. Caballero, Column Generation Framework of Nonlinear Similarity Model for Reconstructing Sibling Groups, INFORMS Journal of Computing, 27(1), 35-47, 2015.

  9. Eduard C. Dragut, Brian P. Beirne, Bhaskar DasGupta, Ali Neyestani, Badr Atassi, Clement Yu and Weiyi Meng, Merging Query Results From Local Search Engines for Geo-referenced Objects, ACM Transactions on the Web, 8(4), 20:1-20:29, 2014.

  10. Bhaskar DasGupta and Lakshmi Kaligounder, On Global Stability of Financial Networks, Journal of Complex Networks, 2(3), 313-354, 2014.

  11. Piotr Berman, Bhaskar DasGupta, Lakshmi Kaligounder and Marek Karpinski, On the Computational Complexity of Measuring Global Stability of Banking Networks, Algorithmica, 70(4), 595-647, 2014.

    Talks based on the above two result were given at:

    Here are some pdf slides for these results.

  12. Réka Albert, Bhaskar DasGupta and Nasim Mobasheri, Topological implications of negative curvature for biological and social networks, Physical Review E, 89 (3), 032811, 2014.

           Here are some pdf slides for these results.

  13. Bhaskar DasGupta and Devendra Desai, On a Connection Between Small Set Expansions and Modularity Clustering, Information Processing Letters, 114 (7), 349-352, 2014.

  14. Satabdi Aditya, Bhaskar DasGupta and Marek Karpinski, Algorithmic Perspectives of Network Transitive Reduction Problems and their Applications to Synthesis and Analysis of Biological Networks, Biology, 3 (1), 1-21, 2014.

  15. Bhaskar DasGupta and S. Muthukrishnan, Stochastic Budget Optimization in Internet Advertising, Algorithmica, 65 (3), 634-661, 2013.

  16. Réka Albert, Bhaskar DasGupta and Nasim Mobasheri, Some perspectives on network modeling in therapeutic target prediction, Biomedical Engineering and Computational Biology, 5, 17-24, 2013.

  17. Bhaskar DasGupta and Devendra Desai, Complexity of Newman's Community Finding Approach for Social Networks, Journal of Computer and System Sciences, 79, 50-67, 2013.
                      (this paper was also be presented at the ICALP 2011 workshop on Graph algorithms and Applications, Zurich, Switzerland, July 3, 2011).

  18. Marco Comi, Bhaskar DasGupta, Michael Schapira and Venkatakumar Srinivasan, On Communication Protocols that Compute Almost Privately, Theoretical Computer Science, 457, 45-58, 2012.

  19. Réka Albert, Bhaskar DasGupta, Anthony Gitter, Gamze Gürsoy, Rashmi Hegde, Pradyut Pal, Gowri Sangeetha Sivanathan and Eduardo Sontag, A New Computationally Efficient Measure of Topological Redundancy of Biological and Social Networks, Physical Review E, 84 (3), 036117, 2011.

       Author was a junior at Neuqua Valley High School, Naperville, IL at the time of publication.

  20. Chun-An Chou, Wanpracha Chaovalitwongse, Tanya Y. Berger-Wolf, Bhaskar DasGupta and Mary V. Ashley, Capacitated Clustering Problem in Computational Biology: Combinatorial and Statistical Approach for Sibling Reconstruction, Computers & Operations Research, 39, 609-619, 2011.

  21. Saad I. Sheikh, Tanya Y. Berger-Wolf, Ashfaq A. Khokhar, Isabel C. Caballero, Mary V. Ashley, Wanpracha Chaovalitwongse, Chun-An Chou and Bhaskar DasGupta, Combinatorial Reconstruction of Half-sibling Groups from Microsatellite Data, Journal of Bioinformatics and Computational Biology, 8(2), 337-356, 2010.

  22. Mary V. Ashley, Tanya Y. Berger-Wolf, Wanpracha Chaovalitwongse, Bhaskar DasGupta, Ashfaq Khokhar and Saad Sheikh, On Approximating An Implicit Cover Problem in Wild Population Study, Discrete Mathematics, Algorithms and Applications, 2 (1), 21-31, 2010.

  23. Wanpracha Chaovalitwongse, Chun-An Chou, Tanya Berger-Wolf, Bhaskar DasGupta, Saad Sheikh, Mary Ashley and Isabel Caballero, New Optimization Model and Algorithm for Sibling Reconstruction from Genetic Markers, INFORMS Journal of Computing, 22 (2), 180-194, 2010.

  24. Mary Ashley, Tanya Y. Berger-Wolf, Piotr Berman, Wanpracha Chaovalitwongse, Bhaskar DasGupta and Ming-Yang Kao, On Approximating Four Covering and Packing Problems , Journal of Computer and System Sciences, 75 (5), 287-302, 2009.

  25. Mary V. Ashley, Isabel C. Caballero, Wanpracha Chaovalitwongse, Bhaskar DasGupta, Priya Govindan, Saad Sheikh and Tanya Y. Berger-Wolf, KINALYZER, A Computer Program for Reconstructing Sibling Groups, Molecular Ecology Resources, 9 (4), 1127-1131, 2009.

  26. Kedsuda Apichonbancha, Bhaskar Dasgupta, Jin Jun, Ion Mandoiu and Emma Mendonca, A review of the Primer Approximation Multiplex PCR technique for detecting large-scale cancer genome lesions , Current Bioinformatics, 4 (1), 1-7, 2009.

  27. Sema Kachalo, Ranran Zhang, Eduardo Sontag, Réka Albert and Bhaskar DasGupta, NET-SYNTHESIS: A software for synthesis, inference and simplification of signal transduction networks , Bioinformatics, 24 (2), 293-295, 2008.

  28. Piotr Berman and Bhaskar DasGupta, Approximating the Online Set Multicover Problems Via Randomized Winnowing, Theoretical Computer Science, 393 (1-3), 54-71, 2008.

  29. Réka Albert, Bhaskar DasGupta, Riccardo Dondi and Eduardo Sontag, Inferring (Biological) Signal Transduction Networks via Transitive Reductions of Directed Graphs, Algorithmica, 51 (2), 129-159, 2008.

  30. Joe Dundas, T.A. Binkowski, Bhaskar DasGupta and Jie Liang, Topology Independent Protein Structural Alignment , BMC Bioinformatics, 8:388, 2007.

  31. Piotr Berman, Bhaskar DasGupta and Eduardo Sontag, Algorithmic Issues in Reverse Engineering of Protein and Gene Networks via the Modular Response Analysis Method , Annals of the New York Academy of Sciences (volume title: Reverse Engineering Biological Networks: Opportunities and Challenges in Computational Methods for Pathway Inference), 1115, 132-141, 2007.

  32. Piotr Berman, Bhaskar DasGupta, Ming-Yang Kao and Jie Wang, On Constructing An Optimal Consensus Clustering from Multiple Clusterings, Information Processing Letters, 104 (4), 137-145, 2007.

  33. Réka Albert, Bhaskar DasGupta, Riccardo Dondi, Sema Kachalo, Eduardo Sontag, Alexander Zelikovsky and Kelly Westbrooks, A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence, Journal of Computational Biology, 14 (7), 927-949, 2007.

  34. Tanya Y. Berger-Wolf, Saad Sheikh, Bhaskar DasGupta, Mary Ashley, Isabel Caballero and Wanpracha Chaovalitwongse, Reconstructing Sibling Relationships in Wild Populations, Bioinformatics, 23 (13), i49-i56, 2007.

  35. Piotr Berman, Bhaskar DasGupta, Dhruv Mubayi, Robert Sloan, György Turàn and Yi Zhang, The Inverse Protein Folding Problem on 2D and 3D Lattices, Discrete Applied Mathematics, 155 (6-7), 719-732, 2007.

  36. Bhaskar DasGupta, German Andres Enciso, Eduardo Sontag and Yi Zhang, Algorithmic and Complexity Results for Decompositions of Biological Networks into Monotone Subsystems, Biosystems, 90 (1), 161-178, 2007.

  37. Piotr Berman, Bhaskar DasGupta and Eduardo Sontag, Randomized Approximation Algorithms for Set Multicover Problems with Applications to Reverse Engineering of Protein and Gene Networks, Discrete Applied Mathematics, 155 (6-7), 733-749, 2007.

  38. Wanpracha Chaovalitwongse, Tanya Y. Berger-Wolf, Bhaskar DasGupta, and Mary Ashley, Set Covering Approach for Reconstruction of Sibling Relationships, Optimization Methods and Software, 22 (1), 11-24, 2007.

  39. Bhaskar DasGupta, João P. Hespanha, James Riehl and Eduardo Sontag, Honey-pot Constrained Searching with Local Sensory Information , Journal of Nonlinear Analysis: Hybrid Systems and Applications , 65 (9), 1773-1793, 2006.

  40. Derong Liu, Xiaoxu Xiong, Bhaskar DasGupta and Huaguang Zhang, Motif Discoveries in Unaligned Molecular Sequences Using Self-Organizing Neural Networks, IEEE Transactions on Neural Networks, 17 (4), 919-928, 2006.

  41. Bhaskar Dasgupta, Sergio Ferrarini, Uthra Gopalakrishnan and Nisha Raj Paryani, Inapproximability Results for the Lateral Gene Transfer Problem , Journal of Combinatorial Optimization, 11 (4), 387-405, 2006.

  42. Bhaskar DasGupta and Barbara Hammer, On Approximate Learning by Multi-layered Feedforward Circuits , Theoretical Computer Science, 348 (1), 95-127, 2005.

  43. Bhaskar DasGupta, Kishori Konwar, Ion Mandoiu and Alex Shvartsman, DNA-BAR: Distinguisher Selection for DNA Barcoding, Bioinformatics, 21 (16), 3424-2426, 2005.

  44. Derong Liu, Xiaoxu Xiong, Zheng-Guang Hou and Bhaskar DasGupta, Identification of motifs with insertions and deletions in protein sequences using self-organizing neural networks , Neural Networks, 18 (5-6), 835-842, 2005.

  45. Bhaskar DasGupta, Kishori Konwar, Ion Mandoiu and Alex Shvartsman, Highly Scalable Algorithms for Robust String Barcoding , International Journal of Bioinformatics Research & Applications, 1 (2), 145-161, 2005.

  46. Piotr Berman, Bhaskar DasGupta and Ming-Yang Kao, Tight Approximability Results for Test Set Problems in Bioinformatics , Journal of Computer and System Sciences, 71 (2), 145-162, 2005.

  47. Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao and Michael Snyder, Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search, Journal of Computational Biology, 11 (4), 766-785, 2004.

  48. Piotr Berman, Bhaskar DasGupta and S. Muthukrishnan, Approximation Algorithms For MAX-MIN Tiling, Journal of Algorithms, 47 (2), 122-134, 2003.
                      (This was one of the top 10 most downloaded article from Journal of Algorithms in 2003)

  49. Frank K. Hwang, Yi-Ching Yao and Bhaskar DasGupta, Some permutation routing algorithms for lower-dimensional hypercubes, Theoretical Computer Science, 270 (1-2), 111-124, 2002.

  50. Piotr Berman, Bhaskar DasGupta and S. Muthukrishnan, Exact Size of the Binary Space Partitioning and Improved Rectangle Tiling Algorithms, SIAM Journal of Discrete Mathematics, 15 (2), 252-267, 2002.

  51. Piotr Berman, Bhaskar DasGupta, S. Muthukrishnan and Suneeta Ramaswami, Efficient Approximation Algorithms for Tiling and Packing Problems With Rectangles, Journal of Algorithms, 41 (2), 443-470, 2001.

  52. Bhaskar DasGupta and Michael A. Palis, Online Real-Time Preemptive Scheduling of Jobs with Deadlines on Multiple Machines, Journal of Scheduling, 4, 297-312, 2001.

  53. Bhaskar DasGupta and Eduardo D. Sontag, A Polynomial-Time Algorithm for Checking Equivalence Under Certain Semiring Congruences motivated by the State-space Isomorphism Problem for Hybrid Systems, Theoretical Computer Science, 262 (1), 161-189, 2001.

  54. Xinzhen Cheng, Bhaskar DasGupta and Bing Lu, Polynomial Time Approximation Scheme for the Symmetric Rectilinear Steiner Arborescence Problem, Journal of Global Optimization, 21 (4), 385-396, 2001.

  55. Piotr Berman and Bhaskar DasGupta, Multi-phase Algorithms for Throughput Maximization for Real-Time Scheduling, Journal of Combinatorial Optimization, 4 (3), 307-323, 2000.

  56. Gerard J. Chang, Bhaskar DasGupta, Wayne M. Dymàcek, Martin Fürer, Matthew Koerlin, Yueh-Shin Lee and Tom Whaley, Characterizations of Bipartite Steinhaus Graphs, Discrete Mathematics, 199 (1-3), 11-25, 1999.

  57. Bhaskar DasGupta and Michael A. Palis, Provably Good Algorithms for Transmission Scheduling in WDM Optical Networks. Journal of Parallel and Distributed Computing, 57 (3), 345-357, 1999.

  58. Bhaskar DasGupta, Xin He, Tao Jiang, Ming Li and John Tromp, On the Linear-Cost Subtree-Transfer Distance between Phylogenetic Trees, Algorithmica, 25 (2), 176-195, 1999.

  59. Bhaskar DasGupta, Tao Jiang, Sampath Kannan, Ming Li and Elizabeth Sweedyk, On the Complexity and Approximation of Syntenic Distance, Discrete Applied Mathematics, 88 (1-3), 59-82, 1998.

  60. Prosenjit Gupta, Ravi Janardan, Michiel Smid and Bhaskar DasGupta, The rectangle enclosure and point-dominance problems revisited, International Journal of Computational Geometry and Applications, 7 (5), 437-455, 1997.

  61. Piotr Berman and Bhaskar DasGupta, On the Complexities of Efficient Solutions of the Rectlinear Polygon Cover Problems , Algorithmica, 17 (4), 331-356, 1997.

  62. Bhaskar DasGupta and Eduardo D. Sontag, Sample Complexity for Learning Recurrent Perceptron Mappings, IEEE Transactions on Information Theory, 42 (5), 1479-1487, 1996.

  63. Bhaskar DasGupta and Georg Schnitger, Analog versus Discrete Neural Networks, Neural Computation, 8 (4), 805-818, 1996.

  64. Bhaskar DasGupta, Hava T. Siegelmann and Eduardo Sontag, On the Complexity of Training Neural Networks with Continuous Activation Functions, IEEE Transactions on Neural Networks, 6 (6), 1490-1504, 1995.

  65. Sudeb Pal, Bhaskar DasGupta and C.E. Veni Madhavan, Optimal Polygon Placement by Translation, International Journal of Computer Mathematics, 52, 139-148, 1994.

  66. Bhaskar DasGupta and C.E. Veni Madhavan, An Approximate Algorithm for the Minimal Vertex Nested Polygon Problem, Information Processing Letters, 33 (1), 35-44, 1989.


"Conference with published proceedings" (in reverse chronological order)
  1. Bhaskar DasGupta, Topological implications of negative curvature for biological networks, 2018 IEEE 8th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2018), p. 54, ©IEEE, 2018.

  2. Andreas D. M. Gunawan, Bhaskar DasGupta and Louxin Zhang, Locating a Tree in a Reticulation-Visible Network in Cubic Time, in 20th Annual International Conference on Research in Computational Molecular Biology, LNBI 9649, M. Singh (ed.), p. 266, Springer, 2016 ; full version at arXiv:1507.02119v2

  3. Cao Yu and Bhaskar DasGupta, Liquidity and Resilience of Credit Network: A Simulation Study, 12th International Conference on Applied Computing, 151-158, IADIS Press, 2015.

  4. Eduard Dragut, Brian Beirne, Ali Neyestani, Badr Atassi, Clement Yu, Bhaskar DasGupta and Weiyi Meng, YumiInt --- A Deep Web Integration System for Local Search Engines for Geo-referenced Objects, 29th IEEE International Conference on Data Engineering, 1352-1355, 2013.

  5. Daniel Ayala, Ouri Wolfson, Bo Xu, Bhaskar Dasgupta and Jie Lin, Pricing of Parking for Congestion Reduction, 20th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems, 2012.

  6. Daniel Ayala, Ouri Wolfson, Bo Xu, Bhaskar Dasgupta and Jie Lin, Spatio-temporal Matching Algorithms for Road Networks, 20th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems, 2012.

  7. Bhaskar DasGupta, Models and Algorithmic Tools for Computational Processes in Cellular Biology: Recent Developments and Future Directions, International Symposium on Bioinformatics Research and Applications 2012, L. Bleris et al. (editors), LNBI 7292, 84-86, Springer-Verlag, 2012.

  8. Daehan Won, Chun-An Chou, Wanpracha Chaovalitwongse, Tanya Berger-Wolf, Bhaskar Dasgupta, Ashfaq Khokhar, Marco Maggioni, Mary Ashley, Jason Palagi and Saad Sheikh, An Integrated Optimization Framework for Inferring Two Generation Kinships and Parental Genotypes from Microsatellite Samples, ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 392-399, 2012.

  9. Daniel Ayala, Ouri Wolfson, Bo Xu, Bhaskar Dasgupta and Jie Lin, Parking in Competitive Settings: A Gravitational Approach, 13th International Conference on Mobile Data Management, IEEE Press, 27-31, 2012.

  10. Daniel Ayala, Ouri Wolfson, Bo Xu, Bhaskar Dasgupta and Jie Lin, Parking Slot Assignment Games, 19th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems, 299-308, 2011.

  11. Marco Comi, Bhaskar DasGupta, Michael Schapira, Venkatakumar Srinivasan, On Communication Protocols that Compute Almost Privately, 4th Symposium on Algorithmic Game Theory, G. Persiano (Ed.), LNCS 6982, Springer-Verlag, 44-56, 2011 (full version at arXiv:1102.1443v2 [cs.CR]).

  12. Amitabha Bhattacharya, Bhaskar DasGupta, Dhruv Mubayi and György Turàn, On Approximate Horn Formula Minimization, 37th International Colloquium on Automata, Languages and Programming (ICALP), S. Abramsky et al. (eds.), Part I, LNCS 6198, 438-450, © Springer-Verlag Berlin Heidelberg, 2010.

  13. Saad I. Sheikh, Tanya Y. Berger-Wolf, Ashfaq Khokhar, Isabel C. Caballero, Mary V. Ashley, Wanpracha Chaovalitwongse and Bhaskar DasGupta, Combinatorial Reconstruction of Half-Sibling Groups, Computational Systems Bioinformatics (proceedings of the CSB 2009 conference), 8, P. Markstein and Y. Xu (editors), © Life Sciences Society, 59-67, 2009.

  14. Piotr Berman, Bhaskar DasGupta and Marek Karpinski, Approximating Transitive Reduction Problems for Directed Networks, 11th Algorithms and Data Structures Symposium (WADS), F. Dehne, M. Gavrilova, J.-R. Sack and C. D. Tóth (eds.), LNCS 5664, 74-85, 2009.

  15. Mary V. Ashley, Tanya Y. Berger-Wolf, Wanpracha Chaovalitwongse, Bhaskar DasGupta, Ashfaq Khokhar and Saad Sheikh, On Approximating An Implicit Cover Problem in Biology, 5th International Conference on Algorithmic Aspects in Information and Management (AAIM), A. Goldberg and Y. Zhou (Eds.), LNCS 5564, 43-54, ©Springer-Verlag Berlin Heidelberg, 2009.

  16. Saad I. Sheikh, Tanya Y. Berger-Wolf, Mary V. Ashley, Isabel C. Caballero, Wanpracha Chaovalitwongse and Bhaskar DasGupta, Error Tolerant Sibship Reconstruction in Wild Populations, Computational Systems Bioinformatics (7th Annual International Conference on Computational Systems Bioinformatics, 26-29 August 2008), P. Markstein and Y. Xu (editors), 273-284, World Scientific Publishers, 2008.

  17. Bhaskar DasGupta, Jin Jun and Ion Mandoiu, Primer Selection Methods for Detection of Genomic Inversions and Deletions via PAMP, Series on Advances in Bioinformatics and Computational Biology (6th Asia Pacific Bioinformatics Conference, Kyoto, Japan, 14-17 January 2008), A. Brazma, S. Miyano and T. Akutsu (editors), 6, 353-362, Imperial College Press, London, 2008.
                      (this paper was also presented in 1st RECOMB Satellite Workshop on Computational Cancer Biology, September 18-20, 2007)

  18. Réka Albert, Bhaskar DasGupta, Riccardo Dondi, Sema Kachalo, Eduardo Sontag, Alexander Zelikovsky and Kelly Westbrooks, A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence, 7th Workshop on Algorithms in Bioinformatics (WABI), R. Giancarlo and S. Hannenhalli (Eds.), LNBI 4645, © Springer-Verlag Berlin Heidelberg, 407-419, 2007.
                      (this paper was also presented at the 2007 Microsoft eScience Workshop at RENCI, Chapel Hill, NC, October 21-23, 2007)

  19. Joe Dundas, T.A. Binkowski, Bhaskar DasGupta and Jie Liang, Topology Independent Protein Structural Alignment, 7th Workshop on Algorithms in Bioinformatics (WABI), R. Giancarlo and S. Hannenhalli (Eds.), LNBI 4645, © Springer-Verlag Berlin Heidelberg, 171-182, 2007.

  20. Tanya Y. Berger-Wolf, Saad Sheikh, Bhaskar DasGupta, Mary Ashley, Isabel Caballero and Wanpracha Chaovalitwongse, Reconstructing Sibling Relationships in Wild Populations, 15th Annual Conference on Intelligent Systems in Molecular Biology (ISMB), 2007.

  21. Bhaskar DasGupta, German Andres Enciso, Eduardo Sontag and Yi Zhang, Algorithmic and Complexity Results for Decompositions of Biological Networks into Monotone Subsystems, 5th International Workshop Experimental Algorithms (WEA), LNCS 4007, 253-264, Springer-Verlag, 2006.

  22. Piotr Berman and Bhaskar DasGupta, Approximating the Online Set Multicover Problems Via Randomized Winnowing, 9th Workshop on Algorithms and Data Structures (WADS), F. Dehne, A. Lòpez-Ortiz and J. R. Sack (editors), LNCS 3608, Springer-Verlag, 110-121, 2005.
                      (A complete version of the paper with all the proofs is here)

  23. Xiaoxu Xiong, Derong Liu and Bhaskar DasGupta, A Self-Organizing Neural Network Structure for Motif Identification in DNA Sequences, IEEE International Conference on Networking, Sensing and Control, 129-134, 2005.

  24. Tanya Y. Berger-Wolf, Bhaskar DasGupta, Wanpracha Chaovalitwongse and Mary Ashley, Combinatorial Reconstructions of Sibling Relationships, 6th International Symposium on Computational Biology and Genome Informatics (CBGI), 1252-1255, 2005.

  25. Bhaskar DasGupta, Sergio Ferrarini, Uthra Gopalakrishnan and Nisha Raj Paryani, Inapproximability Results for the Lateral Gene Transfer Problem, 9th Italian Conference on Theoretical Computer Science (ICTCS'05), M. Coppo et al. (Eds.), LNCS 3701, Springer-Verlag, 182-195, 2005.

  26. Bhaskar DasGupta, Kishori Konwar, Ion Mandoiu and Alex Shvartsman, Highly Scalable Algorithms for Robust String Barcoding, 2005 International Workshop on Bioinformatics Research and Applications (IWBRA), LNCS 3515, V. S. Sunderam, G. D. van Albada, P. M. A. Sloot, et al. (editors), Springer Verlag, 1020-1028, 2005.

  27. Bhaskar DasGupta, João P. Hespanha and Eduardo Sontag, Computational Complexities of Honey-pot Searching with Local Sensory Information, 2004 American Control Conference (ACC 2004), 2134-2138, 2004.

  28. Bhaskar DasGupta, João P. Hespanha and Eduardo Sontag, Aggregation-based Approaches to Honey-pot Searching with Local Sensory Information, 2004 American Control Conference (ACC 2004), 1202-1207, 2004.

  29. T. Andrew Binkowski, Bhaskar DasGupta and Jie Liang, Order independent structural alignment of circularly permutated proteins, 26th Annual International Conference IEEE Engineering in Medicine and Biology Society (EMBS 2004), 2781-2784, 2004.

  30. Piotr Berman, Bhaskar DasGupta and Eduardo Sontag, Randomized Approximation Algorithms for Set Multicover Problems with Applications to Reverse Engineering of Protein and Gene Networks, 7th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems (APPROX), LNCS 3122, K. Jansen, S. Khanna, J. D. P. Rolim and D. Ron (eds.), Springer Verlag, 39-50, 2004.
                      (A revised journal version with somewhat improved bounds is available here)

  31. Piotr Berman, Bhaskar DasGupta and Ming-Yang Kao, Tight Approximability Results for Test Set Problems in Bioinformatics, 9th Scandinavian Workshop on Algorithm Theory (SWAT), LNCS 3111, T. Hagerup and J. Katajainen (eds.), Springer Verlag, 39-50, 2004.

  32. Piotr Berman, Bhaskar DasGupta, Dhruv Mubayi, Robert Sloan, György Turàn and Yi Zhang, The Protein Sequence Design Problem in Canonical Model on 2D and 3D Lattices, 15th Annual Combinatorial Pattern Matching Symposium (CPM), LNCS 3109, C. S. Sahinalp, S. Muthukrishnan and U. Dogrusoz (eds.), 244-253, 2004.

  33. Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao and Michael Snyder, Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search, 2nd International Workshop on Algorithms in Bioinformatics (WABI 2002), LNCS 2452, R. Guigó and D. Gusfield (eds.), Springer Verlag, 419-433, 2002.

  34. Piotr Berman, Bhaskar DasGupta and S. Muthukrishnan, Slice and Dice: A Simple, Improved Approximate Tiling Recipe, 13th ACM-SIAM Symposium on Discrete Algorithms, 455-464, 2002.

  35. Piotr Berman, Bhaskar DasGupta and S. Muthukrishnan, Simple Approximation Algorithm for Nonoverlapping Local Alignments, 13th ACM-SIAM Symposium on Discrete Algorithms, 677-678, 2002.

  36. Piotr Berman, Bhaskar DasGupta, S. Muthukrishnan and Suneeta Ramaswami, Improved Approximation Algorithms for Rectangle Tiling and Packing, 12th ACM-SIAM Symposium on Discrete Algorithms, 427-436, 2001.

  37. Piotr Berman and Bhaskar DasGupta, Improvements in Throughput Maximization for Real-Time Scheduling, 32nd Annual ACM Symposium on Theory of Computing, 680-687, 2000.

  38. Bhaskar DasGupta and Barbara Hammer, On Approximate Learning by Multi-layered Feedforward Circuits, Lecture Notes in Artificial Intelligence 1968, 11th International Conference on Algorithmic Learning Theory, 264-278, 2000.

  39. Bhaskar DasGupta and Michael A. Palis, Online Real-Time Preemptive Scheduling of Jobs with Deadlines, 3rd International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, Lecture Notes in Computer Science (LNCS) 1913, Springer, 96-107, 2000.

  40. Bhaskar DasGupta and Eduardo D. Sontag, A Polynomial-Time Algorithm for an Equivalence Problem which Arises in Hybrid Systems Theory, 37th IEEE Conference on Decision and Control, IEEE Publications, 1629-1634, 1998.

  41. Bhaskar DasGupta and Michael A. Palis, Scheduling Transmissions in WDM Optical Networks, International Conference on Parallel and Distributed Techniques and Applications, 1042-1049, 1998.

  42. Bhaskar DasGupta, Tao Jiang, Sampath Kannan, Ming Li and Elizabeth Sweedyk, On the Complexity and Approximation of Syntenic Distance, 1st Annual International Conference On Computational Molecular Biology, 99-108, 1997.

  43. Bhaskar DasGupta, Xin He, Tao Jiang, Ming Li, John Tromp and Louxin Zhang, On Distances between Phylogenetic Trees, 8th Annual ACM-SIAM Symposium on Discrete Algorithms, 427-436, 1997.

  44. Bhaskar DasGupta and Eduardo D. Sontag, Learning Recurrent Perceptron Mappings, in D. S. Touretzky, M. Mozer and M. E. Hasselmo (eds.), Advances in Neural Information Processing Systems 8, The MIT Press, Cambridge, MA, 204-210, 1996.

  45. Prosenjit Gupta, Ravi Janardan, Michiel Smid and Bhaskar DasGupta, The rectangle enclosure and point-dominance problems revisited, 11th ACM Symposium on Computational Geometry, 162-171, 1995.

  46. Bhaskar DasGupta, Hava T. Siegelmann and Eduardo Sontag, On a Learnability Question Associated to Neural Networks with Continuous Activations, 7th ACM Conference on Learning Theory, 47-56, 1994.

  47. Bhaskar DasGupta and Georg Schnitger, The Power of Approximating: A Comparison of Activation Functions, in C. L. Giles. S. J. Hanson and J. D. Cowan (eds.), Advances in Neural Information Processing Systems 5, Morgan Kaufmann Publishers, 615-622, 1993.

  48. Piotr Berman and Bhaskar DasGupta, On Approximating the Rectlinear Polygon Covering Problems, 4th Canadian Conference on Computational Geometry, 229-235, 1992.

  49. Bhaskar DasGupta, Learning Capabilities of Recurrent Neural Networks, Proceedings of IEEE SouthEastcon, 822-823, 1992.

  50. Sudeb Pal, Bhaskar DasGupta and C.E. Veni Madhavan, Optimal Polygon Placement by Translation, 2nd Canadian Conference on Computational Geometry, 164-171, 1990.

"Chapter in edited books" (in reverse chronological order)
  1. Bhaskar DasGupta and Venkatkumar Srinivasan, A Review of Several Optimization Problems Related to Security in Networked System, in Operations Research, Engineering, and Cyber Security : Trends in Applied Mathematics and Technology, N. J. Daras and Th. M. Rassias (editors), Springer Optimization and Its Applications series, 113, 155-166, 2017.

  2. Sima Behpour and Bhaskar DasGupta, Algorithmic Perspectives of the String Barcoding Problems, in Pattern Recognition in Computational Molecular Biology: Techniques and Approaches, M. Elloumi, C. S. Iliopoulos, J. T. L. Wang and A. Y. Zomaya (editors), 28-42, Wiley Book Series on Bioinformatics: Computational Techniques and Engineering, John Wiley & Sons Ltd., 2015.

  3. Bhaskar DasGupta and Lakshmi Kaligounder, Densely Entangled Financial Systems, in Network Models in Economics and Finance, V. Kalyagin, P. M. Pardalos and Th. M. Rassias (editors), Springer Optimization and Its Applications series 100, 85-105, Springer, 2014.

  4. Bhaskar DasGupta, Computational Complexities of Optimization Problems Related to Model Based Clustering of Networks, in Optimization in Science and Engineering - in Honor of the 60th Anniversary of Birth of Panos Pardalos, S. Butenko, C. Floudas and Th. M. Rassias (editors), 97-113, Springer, 2014.

  5. Bhaskar DasGupta and Venkatkumar Srinivasan, A review of some approximate privacy measures of multi-agent communication protocols, in Frontiers of Intelligent Control and Information Processing, Derong Liu, Cesare Alippi, Dongbin Zhao, and Huaguang Zhang (editors), Chapter 10, 267-283, World Scientific Publishing, 2014.

  6. Bhaskar DasGupta and Lakshmi Kaligounder, A Survey on Fingerprint Classification Methods for Biological Sequences, in Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data (1st edition), A. Zomaya and M. Elloumi (editors), Chapter 28, 645-655, John Wiley and Sons, 2013.

  7. Bhaskar DasGupta, Joseph Dundas and Jie Liang, Algorithmic Methodologies for Discovery of Non-sequential Protein Structure Similarities, in Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics, 1st edition, Chapter 15, Y. Pan, J. Wang and M. Li (editors), Wiley book series on Bioinformatics, John Wiley and Sons, 299-316, 2013.

  8. Bhaskar DasGupta and Derong Liu, Approximate learning of dynamic models/systems, in Encyclopedia of the Sciences of Learning, N. M. Seel (Editor-in-Chief), 291-293, Springer Verlag, 2012.

  9. Joe Dundas, Bhaskar DasGupta, and Jie Liang, Sequence Order Independent Comparison of Protein Global Backbone Structures and Local Binding Surfaces for Evolutionary and Functional Inference, Protein Function Prediction for Omics Era, D. Kihara (editor), 125-143, Springer-Verlag, 2011.

  10. Bhaskar DasGupta, Paola Vera-Licona and Eduardo Sontag, Reverse Engineering of Molecular Networks from a Common Combinatorial Approach, in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, Chapter 40, M. Elloumi and A. Zomaya (editors), John Wiley & Sons, Inc., 2011.

  11. Bhaskar DasGupta, Ming-Yang Kao and Ion Mandoiu, Algorithmic Issues in DNA Barcoding Problems, in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, Chapter 7, M. Elloumi and A. Zomaya (editors), John Wiley & Sons, Inc., 2011.

  12. Réka Albert, Bhaskar DasGupta and Eduardo Sontag, Inference of signal transduction networks from double causal evidence , Methods in Molecular Biology: Topics in Computational Biology, D. Fenyo (ed.), 673, Chapter 16, © Springer Science+Business Media, LLC, 2010.

  13. Mary. Ashley, Tanya Y. Berger-Wolf, Isabel Caballero, Wanpracha Chaovalitwongse, Chun-An Chou, Bhaskar DasGupta and Saad Sheikh, Full Sibling Reconstructions in Wild Populations From Microsatellite Genetic Markers, in Computational Biology: New Research, A. S. Russe (editor), Nova Science Publishers, 231-258, 2009.

  14. Bhaskar DasGupta and Lusheng Wang, Biology Computing, in B. W. Wah (Ed.), Wiley Encyclopedia of Computer Science and Engineering, 1, 336-346, John Wiley & Sons, Inc., 2009.

  15. Bhaskar DasGupta and Ming-Yang Kao, Efficient combinatorial algorithms for DNA sequence processing, in Bioinformatics Algorithms: Techniques and Applications, in Wiley Book Series on Bioinformatics: Computational Techniques and Engineering, A. Zelikovsky and I. Mandoiu (eds), John Wiley & Sons, Inc., 223-238, 2008.

  16. Bhaskar DasGupta, Xin He, Tao Jiang, Ming Li, John Tromp and Louxin Zhang, Nearest Neighbor Interchange and Related Distances, Encyclopedia of Algorithms, M.-Y. Kao (editor), Springer-Verlag, 573-576, 2008.

  17. Bhaskar DasGupta, Derong Liu and Hava Siegelmann, Neural Networks , in Handbook on Approximation Algorithms and Metaheuristics, T. F. Gonzalez (editor), Chapman & Hall/CRC (Computer & Information Science Series), pp. 22-1---22--14, 2007.

  18. Piotr Berman, Bhaskar DasGupta and Eduardo Sontag, Computational Complexities of Combinatorial Problems With Applications to Reverse Engineering of Biological Networks, Advances in Computational Intelligence: Theory and Applications, F.-Y. Wang and D. Liu (eds.), Series in Intelligent Control and Intelligent Automation, 5, World Scientific publishers, 303-316, 2006.

  19. Karhan Akcoglu, James Aspnes, Bhaskar DasGupta and Ming-Yang Kao, Opportunity Cost Algorithms for Combinatorial Auctions, in Applied Optimization: Computational Methods in Decision-Making, Economics and Finance, E. J. Kontoghiorghes, B. Rustem and S. Siokos (eds.), Kluwer Academic Publishers, 455-479, 2002.

  20. Piotr Berman and Bhaskar DasGupta, A Simple Approximation Algorithm for Nonoverlapping Local Alignments (Weighted Independent Sets of Axis Parallel Rectangles) in Biocomputing, 1, P. M. Pardalos and J. Principe (eds.), Kluwer Academic Publishers, 129-138, 2002.

  21. Bhaskar DasGupta and Georg Schnitger, On the Computational Power of Analog Neural Networks, in The Handbook of Brain Theory and Neural Networks, 2nd edition, M. A. Arbib (Editor), Cambridge, MA: The MIT Press, 97-100, 2002.

  22. Bhaskar DasGupta, Xin He, Tao Jiang, Ming Li, John Tromp and Louxin Zhang, On Computing the Nearest Neighbor Interchange Distance, in D. Z. Du, P M. Pardalos and J. Wang (eds.), Proceedings of the DIMACS Workshop on Discrete Problems with Medical Applications, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, American Mathematical Society, 55, 125-143, 2000.

  23. Bhaskar DasGupta and Lusheng Wang, Biology Computing, in J. Webster (Editor), Wiley Encyclopedia of Electrical Engineering and Electronics, John Wiley & Sons, Inc., 386-394, 1999.

  24. Bhaskar DasGupta, Xin He, Tao Jiang, Ming Li, John Tromp, Lusheng Wang and Louxin Zhang, Computing Distances between Evolutionary Trees, in D. Z. Du and P.M. Pardalos (eds.), Handbook of Combinatorial Optimization, Kluwer Academic Publishers, 2, 35-76, 1998.

  25. Bhaskar DasGupta, Hava T. Siegelmann and Eduardo Sontag, On the Intractability of Loading Neural Networks, in V. P. Roychowdhury, K. Y. Siu and A. Orlitsky (eds.), Theoretical Advances in Neural Computation and Learning, Kluwer Academic Publishers, 357-389, 1994.

  26. Bhaskar DasGupta and Vwani P. Roychowdhury, Two Geometric Optimization Problems, in D.-Z. Du and J. Sun (eds.), New Advances in Optimization and Approximation, Kluwer Academic Publishers, 30-57, 1994.

  27. Sourav Bhattacharya and Bhaskar DasGupta, Steiner Problem in Multistage Computer Networks, in D.-Z. Du and P. M. Pardalos (eds.), Network Optimization Problems, World Scientific Publishing Co., 387-401, 1993.

"Unpublished but cited technical reports" (in reverse chronological order)
  1. Bhaskar DasGupta, Ravi Janardan and Naveed Sherwani, On the Greedy Algorithm for a Covering Problem, Technical Report # TR 93-13, Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, February 1993.

  2. Bhaskar DasGupta and Georg Schnitger, Efficient Approximation with Neural Networks: A Comparison of Gate Functions, Technical Report, Pennsylvania State University, June, 1992.

"Conference/workshops without published proceedings" (in reverse chronological order)
  1. Daniel Ayala, Ouri Wolfson, Bo Xu, Bhaskar Dasgupta and Jie Lin, Stability of Marriage and Vehicular Parking, 2nd International Workshop on Matching Under Preferences, Budapest, Hungary, July 10-20, 2012.

  2. Saad I. Sheikh, Tanya Y. Berger-Wolf, Ashfaq A. Khokhar and Bhaskar DasGupta, Consensus Methods for Reconstruction of Sibling Relationships from Genetic Data, 4th Multidisciplinary Workshop on Advances in Preference Handling, Chicago, IL, 2008.

  3. Mary Ashley, Tanya Berger-Wolf, Piotr Berman, Wanpracha Chaovalitwongse, Bhaskar DasGupta and Ming-Yang Kao, Approximating Several Covering/Packing Problems, International Symposium on Combinatorial Optimization 2008, University of Warwick, Coventry, UK, 2008.

  4. Piotr Berman and Bhaskar DasGupta, On Approximating the Corner Cover Problems, 2nd CGC workshop on Computational Geometry, Duke University, October 1997.

  5. Bhaskar DasGupta and Martin Fürer, Counting Bipartite Steinhaus Graphs, 7th SIAM Conference on Discrete Mathematics, 1994.



Publications by "broad" topics (some papers may span over more than one topic)

Computational finance

Computational economics

Social networks

Privacy and Security

Learning theory, Neural nets and circuit complexity
Online algorithms
Computational biology
Scheduling
Computational geometry
Hybrid systems
Set covering / multi-covering
Networks / routing / navigation
Clustering

Graph theory
Miscellaneous


"Computational finance" (reverse chronological order)
  1. Cao Yu and Bhaskar DasGupta, Liquidity and Resilience of Credit Network: A Simulation Study, 12th International Conference on Applied Computing, 151-158, IADIS Press, 2015.

  2. Bhaskar DasGupta and Lakshmi Kaligounder, Densely Entangled Financial Systems, in Network Models in Economics and Finance, V. Kalyagin, P. M. Pardalos and Th. M. Rassias (editors), Springer Optimization and Its Applications series 100, 85-105, Springer, 2014.

  3. Bhaskar DasGupta and Lakshmi Kaligounder, On Global Stability of Financial Networks, Journal of Complex Networks, 2(3), 313-354, 2014.

  4. Piotr Berman, Bhaskar DasGupta, Lakshmi Kaligounder and Marek Karpinski, On the Computational Complexity of Measuring Global Stability of Banking Networks, Algorithmica, 70(4), 595-647, 2014.

    Talks based on the above two results were given at:

    Here are some pdf slides for these results.


"Computational economics" (reverse chronological order)
  1. Bhaskar DasGupta and S. Muthukrishnan, Stochastic Budget Optimization in Internet Advertising, Algorithmica, 65 (3), 634-661, 2013.

  2. Karhan Akcoglu, James Aspnes, Bhaskar DasGupta and Ming-Yang Kao, Opportunity Cost Algorithms for Combinatorial Auctions, in Applied Optimization: Computational Methods in Decision-Making, Economics and Finance, E. J. Kontoghiorghes, B. Rustem and S. Siokos (eds.), Kluwer Academic Publishers, 455-479, 2002.


"Social networks" (reverse chronological order)
  1. Bhaskar DasGupta, Nasim Mobasheri and Ismael G. Yero, On analyzing and evaluating privacy measures for social networks under active attack, Information Sciences, 473, 87-100, 2019.

  2. Tanima Chatterjee, Bhaskar DasGupta, Nasim Mobasheri, Venkatkumar Srinivasan and Ismael G. Yero, On the Computational Complexities of Three Privacy Measures for Large Networks Under Active Attack, Theoretical Computer Science, 775, 53-67, 2019.
         Here are some pdf slides for these results (from the talk at 25th LSD & LAW).

  3. Réka Albert, Bhaskar DasGupta and Nasim Mobasheri, Topological implications of negative curvature for biological and social networks, Physical Review E, 89 (3), 032811, 2014.

           Here are some pdf slides for these results.

  4. Bhaskar DasGupta and Devendra Desai, On a Connection Between Small Set Expansions and Modularity Clustering, Information Processing Letters, 114 (7), 349-352, 2014.

  5. Bhaskar DasGupta, Computational Complexities of Optimization Problems Related to Model Based Clustering of Networks, in Optimization in Science and Engineering - in Honor of the 60th Anniversary of Birth of Panos Pardalos, S. Butenko, C. Floudas and Th. M. Rassias (editors), 97-113, Springer, 2014.

  6. Bhaskar DasGupta and Devendra Desai, Complexity of Newman's Community Finding Approach for Social Networks, Journal of Computer and System Sciences, 79, 50-67, 2013.
                      (this paper was also be presented at the ICALP 2011 workshop on Graph algorithms and Applications, Zurich, Switzerland, July 3, 2011).

  7. Réka Albert, Bhaskar DasGupta, Anthony Gitter, Gamze Gürsoy, Rashmi Hegde, Pradyut Pal, Gowri Sangeetha Sivanathan and Eduardo Sontag, A New Computationally Efficient Measure of Topological Redundancy of Biological and Social Networks, Physical Review E, 84 (3), 036117, 2011.

    Author was a junior at Neuqua Valley High School, Naperville, IL at the time of publication.


"Privacy and security" (reverse chronological order)
  1. Bhaskar DasGupta, Nasim Mobasheri and Ismael G. Yero, On analyzing and evaluating privacy measures for social networks under active attack, Information Sciences, 473, 87-100, 2019.

  2. Tanima Chatterjee, Bhaskar DasGupta, Nasim Mobasheri, Venkatkumar Srinivasan and Ismael G. Yero, On the Computational Complexities of Three Privacy Measures for Large Networks Under Active Attack, Theoretical Computer Science, 775, 53-67, 2019.
         Here are some pdf slides for these results (from the talk at 25th LSD & LAW).

  3. Bhaskar DasGupta and Venkatkumar Srinivasan, A Review of Several Optimization Problems Related to Security in Networked System, in Operations Research, Engineering, and Cyber Security : Trends in Applied Mathematics and Technology, N. J. Daras and Th. M. Rassias (editors), Springer Optimization and Its Applications series, 113, 155-166, 2017.

  4. Bhaskar DasGupta and Venkatkumar Srinivasan, A review of some approximate privacy measures of multi-agent communication protocols, in Frontiers of Intelligent Control and Information Processing, D. Liu, C. Alippi, D. Zhao, and H. Zhang (editors), Chapter 10, 267-283, World Scientific Publishing, 2014.

  5. Marco Comi, Bhaskar DasGupta, Michael Schapira and Venkatakumar Srinivasan, On Communication Protocols that Compute Almost Privately, Theoretical Computer Science, 457, 45-58, 2012.

  6. Marco Comi, Bhaskar DasGupta, Michael Schapira, Venkatakumar Srinivasan, On Communication Protocols that Compute Almost Privately, 4th Symposium on Algorithmic Game Theory, G. Persiano (Ed.), LNCS 6982, Springer-Verlag, 44-56, 2011 (full version at arXiv:1102.1443v2 [cs.CR]).

"Learning theory, Neural nets, and circuit complexity" (reverse chronological order)
  1. Bhaskar DasGupta and Derong Liu, Approximate learning of dynamic models/systems, in Encyclopedia of the Sciences of Learning, N. M. Seel (Editor-in-Chief), 291-293, Springer Verlag, 2012.

  2. Bhaskar DasGupta, Derong Liu and Hava Siegelmann, Neural Networks , in Handbook on Approximation Algorithms and Metaheuristics, T. F. Gonzalez (editor), Chapman & Hall/CRC (Computer & Information Science Series), pp. 22-1---22--14, 2007.

  3. Derong Liu, Xiaoxu Xiong, Bhaskar DasGupta and Huaguang Zhang, Motif Discoveries in Unaligned Molecular Sequences Using Self-Organizing Neural Networks, IEEE Transactions on Neural Networks, 17 (4), 919-928, 2006.

  4. Xiaoxu Xiong, Derong Liu and Bhaskar DasGupta, A Self-Organizing Neural Network Structure for Motif Identification in DNA Sequences, IEEE International Conference on Networking, Sensing and Control, 129-134, 2005.

  5. Derong Liu, Xiaoxu Xiong, Zheng-Guang Hou and Bhaskar DasGupta, Identification of motifs with insertions and deletions in protein sequences using self-organizing neural networks , Neural Networks, 18 (5-6), 835-842, 2005.

  6. Bhaskar DasGupta and Barbara Hammer, On Approximate Learning by Multi-layered Feedforward Circuits , Theoretical Computer Science, 348 (1), 95-127, 2005.

  7. Bhaskar DasGupta and Georg Schnitger, On the Computational Power of Analog Neural Networks, in The Handbook of Brain Theory and Neural Networks, 2nd edition, M. A. Arbib (Editor), Cambridge, MA: The MIT Press, 97-100, 2002.

  8. Bhaskar DasGupta and Barbara Hammer, On Approximate Learning by Multi-layered Feedforward Circuits, Lecture Notes in Artificial Intelligence 1968, 11th International Conference on Algorithmic Learning Theory, 264-278, 2000.

  9. Bhaskar DasGupta and Eduardo D. Sontag, Learning Recurrent Perceptron Mappings, in D. S. Touretzky, M. Mozer and M. E. Hasselmo (eds.), Advances in Neural Information Processing Systems 8, The MIT Press, Cambridge, MA, 204-210, 1996.

  10. Bhaskar DasGupta and Eduardo D. Sontag, Sample Complexity for Learning Recurrent Perceptron Mappings, IEEE Transactions on Information Theory, 42 (5), 1479-1487, 1996.

  11. Bhaskar DasGupta and Georg Schnitger, Analog versus Discrete Neural Networks, Neural Computation, 8 (4), 805-818, 1996.

  12. Bhaskar DasGupta, Hava T. Siegelmann and Eduardo Sontag, On the Complexity of Training Neural Networks with Continuous Activation Functions, IEEE Transactions on Neural Networks, 6 (6), 1490-1504, 1995.

  13. Bhaskar DasGupta, Hava T. Siegelmann and Eduardo Sontag, On the Intractability of Loading Neural Networks, in V. P. Roychowdhury, K. Y. Siu and A. Orlitsky (eds.), Theoretical Advances in Neural Computation and Learning, Kluwer Academic Publishers, 357-389, 1994.

  14. Bhaskar DasGupta, Hava T. Siegelmann and Eduardo Sontag, On a Learnability Question Associated to Neural Networks with Continuous Activations, 7th ACM Conference on Learning Theory, 47-56, 1994.

  15. Bhaskar DasGupta and Georg Schnitger, The Power of Approximating: A Comparison of Activation Functions, in C. L. Giles. S. J. Hanson and J. D. Cowan (eds.), Advances in Neural Information Processing Systems 5, Morgan Kaufmann Publishers, 615-622, 1993.

  16. Bhaskar DasGupta and Georg Schnitger, Efficient Approximation with Neural Networks: A Comparison of Gate Functions, Technical Report, Pennsylvania State University, June, 1992.

  17. Bhaskar DasGupta, Learning Capabilities of Recurrent Neural Networks, Proceedings of IEEE SouthEastcon, 822-823, 1992.

"Online set multicover" (reverse chronological order)
  1. Piotr Berman and Bhaskar DasGupta, Approximating the Online Set Multicover Problems Via Randomized Winnowing, Theoretical Computer Science, 393 (1-3), 54-71, 2008.

  2. Piotr Berman and Bhaskar DasGupta, Approximating the Online Set Multicover Problems Via Randomized Winnowing, 9th Workshop on Algorithms and Data Structures (WADS), F. Dehne, A. Lòpez-Ortiz and J. R. Sack (editors), LNCS 3608, Springer-Verlag, 110-121, 2005.
                      (A complete version of the paper with all the proofs is here)

"Online multi-processor scheduling" (reverse chronological order)
  1. Bhaskar DasGupta and Michael A. Palis, Online Real-Time Preemptive Scheduling of Jobs with Deadlines on Multiple Machines, Journal of Scheduling, 4, 297-312, 2001.

  2. Bhaskar DasGupta and Michael A. Palis, Online Real-Time Preemptive Scheduling of Jobs with Deadlines, 3rd International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, Lecture Notes in Computer Science (LNCS) 1913, Springer, 96-107, 2000.

"Computational population biology" (reverse chronological order)
  1. Chun-An Chou, Zhe Liang, Wanpracha Chaovalitwongse, Tanya Y. Berger-Wolf, Bhaskar DasGupta, Saad Sheikh, Mary V. Ashley and Isabel C. Caballero, Column Generation Framework of Nonlinear Similarity Model for Reconstructing Sibling Groups, INFORMS Journal of Computing, 27(1), 35-47, 2015.

  2. Daehan Won, Chun-An Chou, Wanpracha Chaovalitwongse, Tanya Berger-Wolf, Bhaskar Dasgupta, Ashfaq Khokhar, Marco Maggioni, Mary Ashley, Jason Palagi and Saad Sheikh, An Integrated Optimization Framework for Inferring Two Generation Kinships and Parental Genotypes from Microsatellite Samples, ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 392-399, 2012.

  3. Chun-An Chou, Wanpracha Chaovalitwongse, Tanya Y. Berger-Wolf, Bhaskar DasGupta and Mary V. Ashley, Capacitated Clustering Problem in Computational Biology: Combinatorial and Statistical Approach for Sibling Reconstruction, Computers & Operations Research, 39, 609-619, 2011.

  4. Saad I. Sheikh, Tanya Y. Berger-Wolf, Ashfaq A. Khokhar, Isabel C. Caballero, Mary V. Ashley, Wanpracha Chaovalitwongse, Chun-An Chou and Bhaskar DasGupta, Combinatorial Reconstruction of Half-sibling Groups from Microsatellite Data, Journal of Bioinformatics and Computational Biology, 8(2), 337-356, 2010.

  5. Mary V. Ashley, Tanya Y. Berger-Wolf, Wanpracha Chaovalitwongse, Bhaskar DasGupta, Ashfaq Khokhar and Saad Sheikh, On Approximating An Implicit Cover Problem in Wild Population Study, Discrete Mathematics, Algorithms and Applications, 2 (1), 21-31, 2010.

  6. Wanpracha Chaovalitwongse, Chun-An Chou, Tanya Berger-Wolf, Bhaskar DasGupta, Saad Sheikh, Mary Ashley and Isabel Caballero, New Optimization Model and Algorithm for Sibling Reconstruction from Genetic Markers, INFORMS Journal of Computing, 22 (2), 180-194, 2010.

  7. Saad I. Sheikh, Tanya Y. Berger-Wolf, Ashfaq Khokhar, Isabel C. Caballero, Mary V. Ashley, Wanpracha Chaovalitwongse and Bhaskar DasGupta, Combinatorial Reconstruction of Half-Sibling Groups, Computational Systems Bioinformatics (proceedings of the CSB 2009 conference), 8, P. Markstein and Y. Xu (editors), © Life Sciences Society, 59-67, 2009.

  8. Mary Ashley, Tanya Y. Berger-Wolf, Piotr Berman, Wanpracha Chaovalitwongse, Bhaskar DasGupta and Ming-Yang Kao, On Approximating Four Covering and Packing Problems , Journal of Computer and System Sciences, 75 (5), 287-302, 2009.

  9. Mary V. Ashley, Tanya Y. Berger-Wolf, Wanpracha Chaovalitwongse, Bhaskar DasGupta, Ashfaq Khokhar and Saad Sheikh, On Approximating An Implicit Cover Problem in Biology, 5th International Conference on Algorithmic Aspects in Information and Management (AAIM), A. Goldberg and Y. Zhou (Eds.), LNCS 5564, 43-54, ©Springer-Verlag Berlin Heidelberg, 2009.

  10. Mary V. Ashley, Isabel C. Caballero, Wanpracha Chaovalitwongse, Bhaskar DasGupta, Priya Govindan, Saad Sheikh and Tanya Y. Berger-Wolf, KINALYZER, A Computer Program for Reconstructing Sibling Groups, Molecular Ecology Resources, 9 (4), 1127-1131, 2009.

  11. Mary. Ashley, Tanya Y. Berger-Wolf, Isabel Caballero, Wanpracha Chaovalitwongse, Chun-An Chou, Bhaskar DasGupta and Saad Sheikh, Full Sibling Reconstructions in Wild Populations From Microsatellite Genetic Markers, in Computational Biology: New Research, A. S. Russe (editor), Nova Science Publishers, 231-258, 2009.

  12. Saad I. Sheikh, Tanya Y. Berger-Wolf, Mary V. Ashley, Isabel C. Caballero, Wanpracha Chaovalitwongse and Bhaskar DasGupta, Error Tolerant Sibship Reconstruction in Wild Populations, Computational Systems Bioinformatics (7th Annual International Conference on Computational Systems Bioinformatics, 26-29 August 2008), P. Markstein and Y. Xu (editors), 273-284, World Scientific Publishers, 2008.

  13. Saad I. Sheikh, Tanya Y. Berger-Wolf, Ashfaq A. Khokhar and Bhaskar DasGupta, Consensus Methods for Reconstruction of Sibling Relationships from Genetic Data, 4th Multidisciplinary Workshop on Advances in Preference Handling, Chicago, IL, 2008.

  14. Mary Ashley, Tanya Berger-Wolf, Piotr Berman, Wanpracha Chaovalitwongse, Bhaskar DasGupta and Ming-Yang Kao, Approximating Several Covering/Packing Problems, International Symposium on Combinatorial Optimization 2008, University of Warwick, Coventry, UK, 2008 (abstract only).

  15. Tanya Y. Berger-Wolf, Saad Sheikh, Bhaskar DasGupta, Mary Ashley, Isabel Caballero and Wanpracha Chaovalitwongse, Reconstructing Sibling Relationships in Wild Populations, Bioinformatics, 23 (13), i49-i56, 2007.

  16. Wanpracha Chaovalitwongse, Tanya Y. Berger-Wolf, Bhaskar DasGupta, and Mary Ashley, Set Covering Approach for Reconstruction of Sibling Relationships, Optimization Methods and Software, 22 (1), 11-24, 2007.

  17. Tanya Y. Berger-Wolf, Bhaskar DasGupta, Wanpracha Chaovalitwongse and Mary Ashley, Combinatorial Reconstructions of Sibling Relationships, 6th International Symposium on Computational Biology and Genome Informatics (CBGI), 1252-1255, 2005.

"Biological networks" (reverse chronological order)
  1. Bhaskar DasGupta, Topological implications of negative curvature for biological networks, 2018 IEEE 8th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2018), p. 54, ©IEEE, 2018.

  2. (graduate level textbook) Bhaskar DasGupta and Jie Liang, Models and Algorithms for Biomolecules and Molecular Networks, John Wiley & Sons, Inc., 2016

  3. Réka Albert, Bhaskar DasGupta and Nasim Mobasheri, Topological implications of negative curvature for biological and social networks, Physical Review E, 89 (3), 032811, 2014.

           Here are some pdf slides for these results.

  4. Satabdi Aditya, Bhaskar DasGupta and Marek Karpinski, Algorithmic Perspectives of Network Transitive Reduction Problems and their Applications to Synthesis and Analysis of Biological Networks, Biology, 3 (1), 1-21, 2014.

  5. Réka Albert, Bhaskar DasGupta and Nasim Mobasheri, Some perspectives on network modeling in therapeutic target prediction, Biomedical Engineering and Computational Biology, 5, 17-24, 2013.

  6. Bhaskar DasGupta, Models and Algorithmic Tools for Computational Processes in Cellular Biology: Recent Developments and Future Directions, International Symposium on Bioinformatics Research and Applications 2012, L. Bleris et al. (editors), LNBI 7292, 84-86, Springer-Verlag, 2012.

  7. Réka Albert, Bhaskar DasGupta, Anthony Gitter, Gamze Gürsoy, Rashmi Hegde, Pradyut Pal, Gowri Sangeetha Sivanathan and Eduardo Sontag, A New Computationally Efficient Measure of Topological Redundancy of Biological and Social Networks, Physical Review E, 84 (3), 036117, 2011.

    Author was a junior at Neuqua Valley High School, Naperville, IL at the time of publication.

  8. Bhaskar DasGupta, Paola Vera-Licona and Eduardo Sontag, Reverse Engineering of Molecular Networks from a Common Combinatorial Approach, in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, Chapter 40, M. Elloumi and A. Zomaya (editors), John Wiley & Sons, Inc., 2011.

  9. Réka Albert, Bhaskar DasGupta and Eduardo Sontag, Inference of signal transduction networks from double causal evidence , Methods in Molecular Biology: Topics in Computational Biology, D. Fenyo (ed.), 673, Chapter 16, © Springer Science+Business Media, LLC, 2010.

  10. Sema Kachalo, Ranran Zhang, Eduardo Sontag, Réka Albert and Bhaskar DasGupta, NET-SYNTHESIS: A software for synthesis, inference and simplification of signal transduction networks , Bioinformatics, 24 (2), 293-295, 2008.

  11. Réka Albert, Bhaskar DasGupta, Riccardo Dondi and Eduardo Sontag, Inferring (Biological) Signal Transduction Networks via Transitive Reductions of Directed Graphs, Algorithmica, 51 (2), 129-159, 2008.

  12. Réka Albert, Bhaskar DasGupta, Riccardo Dondi, Sema Kachalo, Eduardo Sontag, Alexander Zelikovsky and Kelly Westbrooks, A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence, 7th Workshop on Algorithms in Bioinformatics (WABI), R. Giancarlo and S. Hannenhalli (Eds.), LNBI 4645, © Springer-Verlag Berlin Heidelberg, 407-419, 2007.
                      (this paper was also presented at the 2007 Microsoft eScience Workshop at RENCI, Chapel Hill, NC, October 21-23, 2007)

  13. Piotr Berman, Bhaskar DasGupta and Eduardo Sontag, Algorithmic Issues in Reverse Engineering of Protein and Gene Networks via the Modular Response Analysis Method , Annals of the New York Academy of Sciences (volume title: Reverse Engineering Biological Networks: Opportunities and Challenges in Computational Methods for Pathway Inference), 1115, 132-141, 2007.

  14. Réka Albert, Bhaskar DasGupta, Riccardo Dondi, Sema Kachalo, Eduardo Sontag, Alexander Zelikovsky and Kelly Westbrooks, A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence, Journal of Computational Biology, 14 (7), 927-949, 2007.

  15. Bhaskar DasGupta, German Andres Enciso, Eduardo Sontag and Yi Zhang, Algorithmic and Complexity Results for Decompositions of Biological Networks into Monotone Subsystems, Biosystems, 90 (1), 161-178, 2007.

  16. Piotr Berman, Bhaskar DasGupta and Eduardo Sontag, Randomized Approximation Algorithms for Set Multicover Problems with Applications to Reverse Engineering of Protein and Gene Networks, Discrete Applied Mathematics, 155 (6-7), 733-749, 2007.

  17. Piotr Berman, Bhaskar DasGupta and Eduardo Sontag, Computational Complexities of Combinatorial Problems With Applications to Reverse Engineering of Biological Networks, Advances in Computational Intelligence: Theory and Applications, F.-Y. Wang and D. Liu (eds.), Series in Intelligent Control and Intelligent Automation, 5, World Scientific publishers, 303-316, 2006.

  18. Bhaskar DasGupta, German Andres Enciso, Eduardo Sontag and Yi Zhang, Algorithmic and Complexity Results for Decompositions of Biological Networks into Monotone Subsystems, 5th International Workshop Experimental Algorithms (WEA), LNCS 4007, 253-264, Springer-Verlag, 2006.

  19. Piotr Berman, Bhaskar DasGupta and Eduardo Sontag, Randomized Approximation Algorithms for Set Multicover Problems with Applications to Reverse Engineering of Protein and Gene Networks, 7th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems (APPROX), LNCS 3122, K. Jansen, S. Khanna, J. D. P. Rolim and D. Ron (eds.), Springer Verlag, 39-50, 2004.
                      (A revised journal version with somewhat improved bounds is available here)

"Phylogenetic trees" (reverse chronological order)
  1. Andreas D.M. Gunawan, Bhaskar DasGupta and Louxin Zhang, A Decomposition Theorem and Two Algorithms for Reticulation-Visible Networks, Information and Computation, 252, 161-175, 2017.

  2. Andreas D. M. Gunawan, Bhaskar DasGupta and Louxin Zhang, Locating a Tree in a Reticulation-Visible Network in Cubic Time, in 20th Annual International Conference on Research in Computational Molecular Biology, LNBI 9649, M. Singh (ed.), p. 266, Springer, 2016 ; full version at arXiv:1507.02119v2

  3. Bhaskar DasGupta, Xin He, Tao Jiang, Ming Li, John Tromp and Louxin Zhang, Nearest Neighbor Interchange and Related Distances, Encyclopedia of Algorithms, M.-Y. Kao (editor), Springer-Verlag, 573-576, 2008.

  4. Bhaskar Dasgupta, Sergio Ferrarini, Uthra Gopalakrishnan and Nisha Raj Paryani, Inapproximability Results for the Lateral Gene Transfer Problem , Journal of Combinatorial Optimization, 11 (4), 387-405, 2006.

  5. Bhaskar DasGupta, Sergio Ferrarini, Uthra Gopalakrishnan and Nisha Raj Paryani, Inapproximability Results for the Lateral Gene Transfer Problem, 9th Italian Conference on Theoretical Computer Science (ICTCS'05), M. Coppo et al. (Eds.), LNCS 3701, Springer-Verlag, 182-195, 2005.

  6. Bhaskar DasGupta, Xin He, Tao Jiang, Ming Li, John Tromp and Louxin Zhang, On Computing the Nearest Neighbor Interchange Distance, in D. Z. Du, P M. Pardalos and J. Wang (eds.), Proceedings of the DIMACS Workshop on Discrete Problems with Medical Applications, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, American Mathematical Society, 55, 125-143, 2000.

  7. Bhaskar DasGupta, Xin He, Tao Jiang, Ming Li and John Tromp, On the Linear-Cost Subtree-Transfer Distance between Phylogenetic Trees, Algorithmica, 25 (2), 176-195, 1999.

  8. Bhaskar DasGupta, Xin He, Tao Jiang, Ming Li, John Tromp, Lusheng Wang and Louxin Zhang, Computing Distances between Evolutionary Trees, in D. Z. Du and P.M. Pardalos (eds.), Handbook of Combinatorial Optimization, Kluwer Academic Publishers, 2, 35-76, 1998.

  9. Bhaskar DasGupta, Xin He, Tao Jiang, Ming Li, John Tromp and Louxin Zhang, On Distances between Phylogenetic Trees, 8th Annual ACM-SIAM Symposium on Discrete Algorithms, 427-436, 1997.

"String barcoding and other test set problems" (reverse chronological order)
  1. Sima Behpour and Bhaskar DasGupta, Algorithmic Perspectives of the String Barcoding Problems, in Pattern Recognition in Computational Molecular Biology: Techniques and Approaches, M. Elloumi, C. S. Iliopoulos, J. T. L. Wang and A. Y. Zomaya (editors), 28-42, Wiley Book Series on Bioinformatics: Computational Techniques and Engineering, John Wiley & Sons Ltd., 2015.

  2. Bhaskar DasGupta, Ming-Yang Kao and Ion Mandoiu, Algorithmic Issues in DNA Barcoding Problems, in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, Chapter 7, M. Elloumi and A. Zomaya (editors), John Wiley & Sons, Inc., 2011.

  3. Bhaskar DasGupta, Kishori Konwar, Ion Mandoiu and Alex Shvartsman, Highly Scalable Algorithms for Robust String Barcoding, 2005 International Workshop on Bioinformatics Research and Applications (IWBRA), LNCS 3515, V. S. Sunderam, G. D. van Albada, P. M. A. Sloot, et al. (editors), Springer Verlag, 1020-1028, 2005.

  4. Piotr Berman, Bhaskar DasGupta and Ming-Yang Kao, Tight Approximability Results for Test Set Problems in Bioinformatics , Journal of Computer and System Sciences, 71 (2), 145-162, 2005.

  5. Bhaskar DasGupta, Kishori Konwar, Ion Mandoiu and Alex Shvartsman, Highly Scalable Algorithms for Robust String Barcoding , International Journal of Bioinformatics Research & Applications, 1 (2), 145-161, 2005.

  6. Bhaskar DasGupta, Kishori Konwar, Ion Mandoiu and Alex Shvartsman, DNA-BAR: Distinguisher Selection for DNA Barcoding, Bioinformatics, 21 (16), 3424-2426, 2005.

  7. Piotr Berman, Bhaskar DasGupta and Ming-Yang Kao, Tight Approximability Results for Test Set Problems in Bioinformatics, 9th Scandinavian Workshop on Algorithm Theory (SWAT), LNCS 3111, T. Hagerup and J. Katajainen (eds.), Springer Verlag, 39-50, 2004.

"Protein structures" (reverse chronological order)
  1. (graduate level textbook) Bhaskar DasGupta and Jie Liang, Models and Algorithms for Biomolecules and Molecular Networks, John Wiley & Sons, Inc., 2016

  2. Bhaskar DasGupta, Joseph Dundas and Jie Liang, Algorithmic Methodologies for Discovery of Non-sequential Protein Structure Similarities, in Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics, 1st edition, Chapter 15, Y. Pan, J. Wang and M. Li (editors), Wiley book series on Bioinformatics, John Wiley and Sons, 299-316, 2013.

  3. Joe Dundas, Bhaskar DasGupta, and Jie Liang, Sequence Order Independent Comparison of Protein Global Backbone Structures and Local Binding Surfaces for Evolutionary and Functional Inference, Protein Function Prediction for Omics Era, D. Kihara (editor), 125-143, Springer-Verlag, 2011.

  4. Joe Dundas, T.A. Binkowski, Bhaskar DasGupta and Jie Liang, Topology Independent Protein Structural Alignment , BMC Bioinformatics, 8:388, 2007.

  5. Joe Dundas, T.A. Binkowski, Bhaskar DasGupta and Jie Liang, Topology Independent Protein Structural Alignment, 7th Workshop on Algorithms in Bioinformatics (WABI), R. Giancarlo and S. Hannenhalli (Eds.), LNBI 4645, © Springer-Verlag Berlin Heidelberg, 171-182, 2007.

  6. Piotr Berman, Bhaskar DasGupta, Dhruv Mubayi, Robert Sloan, György Turàn and Yi Zhang, The Inverse Protein Folding Problem on 2D and 3D Lattices, Discrete Applied Mathematics, 155 (6-7), 719-732, 2007.

  7. Piotr Berman, Bhaskar DasGupta, Dhruv Mubayi, Robert Sloan, György Turàn and Yi Zhang, The Protein Sequence Design Problem in Canonical Model on 2D and 3D Lattices, 15th Annual Combinatorial Pattern Matching Symposium (CPM), LNCS 3109, C. S. Sahinalp, S. Muthukrishnan and U. Dogrusoz (eds.), 244-253, 2004.

  8. T. Andrew Binkowski, Bhaskar DasGupta and Jie Liang, Order independent structural alignment of circularly permutated proteins, 26th Annual International Conference IEEE Engineering in Medicine and Biology Society (EMBS 2004), 2781-2784, 2004.

"Sequence alignment" (reverse chronological order)
  1. Bhaskar DasGupta and Ming-Yang Kao, Efficient combinatorial algorithms for DNA sequence processing, in Bioinformatics Algorithms: Techniques and Applications, in Wiley Book Series on Bioinformatics: Computational Techniques and Engineering, A. Zelikovsky and I. Mandoiu (eds), John Wiley & Sons, Inc., 223-238, 2008.

  2. Piotr Berman and Bhaskar DasGupta, A Simple Approximation Algorithm for Nonoverlapping Local Alignments (Weighted Independent Sets of Axis Parallel Rectangles) in Biocomputing, 1, P. M. Pardalos and J. Principe (eds.), Kluwer Academic Publishers, 129-138, 2002.

  3. Piotr Berman, Bhaskar DasGupta and S. Muthukrishnan, Simple Approximation Algorithm for Nonoverlapping Local Alignments, 13th ACM-SIAM Symposium on Discrete Algorithms, 677-678, 2002.

"Genome tiling" (reverse chronological order)
  1. Bhaskar DasGupta and Ming-Yang Kao, Efficient combinatorial algorithms for DNA sequence processing, in Bioinformatics Algorithms: Techniques and Applications, in Wiley Book Series on Bioinformatics: Computational Techniques and Engineering, A. Zelikovsky and I. Mandoiu (eds), John Wiley & Sons, Inc., 223-238, 2008.

  2. Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao and Michael Snyder, Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search, Journal of Computational Biology, 11 (4), 766-785, 2004.

  3. Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao and Michael Snyder, Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search, 2nd International Workshop on Algorithms in Bioinformatics (WABI 2002), LNCS 2452, R. Guigó and D. Gusfield (eds.), Springer Verlag, 419-433, 2002.

"Primer design" (reverse chronological order)
  1. Kedsuda Apichonbancha, Bhaskar Dasgupta, Jin Jun, Ion Mandoiu and Emma Mendonca, A review of the Primer Approximation Multiplex PCR technique for detecting large-scale cancer genome lesions , Current Bioinformatics, 4 (1), 1-7, 2009.

  2. Bhaskar DasGupta, Jin Jun and Ion Mandoiu, Primer Selection Methods for Detection of Genomic Inversions and Deletions via PAMP, Series on Advances in Bioinformatics and Computational Biology (6th Asia Pacific Bioinformatics Conference, Kyoto, Japan, 14-17 January 2008), A. Brazma, S. Miyano and T. Akutsu (editors), 6, 353-362, Imperial College Press, London, 2008.
                      (this paper was also presented in 1st RECOMB Satellite Workshop on Computational Cancer Biology, September 18-20, 2007)

"Genomic distance" (reverse chronological order)
  1. Bhaskar DasGupta, Tao Jiang, Sampath Kannan, Ming Li and Elizabeth Sweedyk, On the Complexity and Approximation of Syntenic Distance, Discrete Applied Mathematics, 88 (1-3), 59-82, 1998.

  2. Bhaskar DasGupta, Tao Jiang, Sampath Kannan, Ming Li and Elizabeth Sweedyk, On the Complexity and Approximation of Syntenic Distance, 1st Annual International Conference On Computational Molecular Biology, 99-108, 1997.

"Fingerprint classification"
  1. Bhaskar DasGupta and Lakshmi Kaligounder, A Survey on Fingerprint Classification Methods for Biological Sequences, in Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data (1st edition), A. Zomaya and M. Elloumi (editors), Chapter 28, 645-655, John Wiley and Sons, 2013.

"Foreword to journal special issues" (reverse chronological order)
  1. Fahad Saeed, Hisham Al-Mubaid and Bhaskar DasGupta, Foreword to the special issue on selected papers from the 6th international conference on Bioinformatics and Computational Biology (BICoB 2014), Journal of Bioinformatics and Computational Biology, 12 (5), 1402001, 2014.

  2. Hisham Al-Mubaid, Bhaskar DasGupta and Fahad Saeed, Foreword to the special issue on selected papers from the 5th international conference on Bioinformatics and Computational Biology (BICoB 2013), Journal of Bioinformatics and Computational Biology, 11 (5), 1302002, 2013.

  3. Piotr Berman, Bhaskar DasGupta and Jie Liang (editors), Foreword to the special issue on Algorithmic Methodologies for Processing Protein Structures, Sequences, and Networks, Algorithmica, 48 (4), p. 301, 2007.

"Miscellaneous (computational biology)" (reverse chronological order)
  1. Farzane Yahyanejad, Bhaskar DasGupta and Réka Albert, A survey of some tensor analysis techniques for biological systems, to appear in Quantitative Biology.

  2. Bhaskar DasGupta and Lusheng Wang, Biology Computing, in B. W. Wah (Ed.), Wiley Encyclopedia of Computer Science and Engineering, 1, 336-346, John Wiley & Sons, Inc., 2009.

  3. Bhaskar DasGupta and Lusheng Wang, Biology Computing, in J. Webster (Editor), Wiley Encyclopedia of Electrical Engineering and Electronics, John Wiley & Sons, Inc., 386-394, 1999.

"Multi-processor scheduling" (reverse chronological order)
  1. Bhaskar DasGupta and Michael A. Palis, Online Real-Time Preemptive Scheduling of Jobs with Deadlines on Multiple Machines, Journal of Scheduling, 4, 297-312, 2001.

  2. Bhaskar DasGupta and Michael A. Palis, Online Real-Time Preemptive Scheduling of Jobs with Deadlines, 3rd International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, Lecture Notes in Computer Science (LNCS) 1913, Springer, 96-107, 2000.

  3. Piotr Berman and Bhaskar DasGupta, Improvements in Throughput Maximization for Real-Time Scheduling, 32nd Annual ACM Symposium on Theory of Computing, 680-687, 2000.

  4. Piotr Berman and Bhaskar DasGupta, Multi-phase Algorithms for Throughput Maximization for Real-Time Scheduling, Journal of Combinatorial Optimization, 4 (3), 307-323, 2000.

"Scheduling in optical networks" (reverse chronological order)
  1. Bhaskar DasGupta and Michael A. Palis, Provably Good Algorithms for Transmission Scheduling in WDM Optical Networks. Journal of Parallel and Distributed Computing, 57 (3), 345-357, 1999.

  2. Bhaskar DasGupta and Michael A. Palis, Scheduling Transmissions in WDM Optical Networks, International Conference on Parallel and Distributed Techniques and Applications, 1042-1049, 1998.

"Polygonal problems in computational geometry" (reverse chronological order)
  1. Piotr Berman and Bhaskar DasGupta, On Approximating the Corner Cover Problems, 2nd CGC workshop on Computational Geometry, Duke University, October 1997 (abstract only).

  2. Piotr Berman and Bhaskar DasGupta, On the Complexities of Efficient Solutions of the Rectlinear Polygon Cover Problems , Algorithmica, 17 (4), 331-356, 1997.

  3. Bhaskar DasGupta and Vwani P. Roychowdhury, Two Geometric Optimization Problems, in D.-Z. Du and J. Sun (eds.), New Advances in Optimization and Approximation, Kluwer Academic Publishers, 30-57, 1994.

  4. Sudeb Pal, Bhaskar DasGupta and C.E. Veni Madhavan, Optimal Polygon Placement by Translation, International Journal of Computer Mathematics, 52, 139-148, 1994.

  5. Piotr Berman and Bhaskar DasGupta, On Approximating the Rectlinear Polygon Covering Problems, 4th Canadian Conference on Computational Geometry, 229-235, 1992.

  6. Sudeb Pal, Bhaskar DasGupta and C.E. Veni Madhavan, Optimal Polygon Placement by Translation, 2nd Canadian Conference on Computational Geometry, 164-171, 1990.

  7. Bhaskar DasGupta and C.E. Veni Madhavan, An Approximate Algorithm for the Minimal Vertex Nested Polygon Problem, Information Processing Letters, 33 (1), 35-44, 1989.

"Rectangle tiling/packing/covering" (reverse chronological order)
  1. Piotr Berman, Bhaskar DasGupta and S. Muthukrishnan, Approximation Algorithms For MAX-MIN Tiling, Journal of Algorithms, 47 (2), 122-134, 2003.
    (This was one of the top 10 most downloaded article from Journal of Algorithms in 2003)

  2. Piotr Berman, Bhaskar DasGupta and S. Muthukrishnan, Exact Size of the Binary Space Partitioning and Improved Rectangle Tiling Algorithms, SIAM Journal of Discrete Mathematics, 15 (2), 252-267, 2002.

  3. Piotr Berman, Bhaskar DasGupta and S. Muthukrishnan, Slice and Dice: A Simple, Improved Approximate Tiling Recipe, 13th ACM-SIAM Symposium on Discrete Algorithms, 455-464, 2002.

  4. Piotr Berman, Bhaskar DasGupta, S. Muthukrishnan and Suneeta Ramaswami, Efficient Approximation Algorithms for Tiling and Packing Problems With Rectangles, Journal of Algorithms, 41 (2), 443-470, 2001.

  5. Piotr Berman, Bhaskar DasGupta, S. Muthukrishnan and Suneeta Ramaswami, Improved Approximation Algorithms for Rectangle Tiling and Packing, 12th ACM-SIAM Symposium on Discrete Algorithms, 427-436, 2001.

"Binary space partitioning"
  1. Piotr Berman, Bhaskar DasGupta and S. Muthukrishnan, Exact Size of the Binary Space Partitioning and Improved Rectangle Tiling Algorithms, SIAM Journal of Discrete Mathematics, 15 (2), 252-267, 2002.

"Point dominance (rectangle enclosure)" (reverse chronological order)
  1. Prosenjit Gupta, Ravi Janardan, Michiel Smid and Bhaskar DasGupta, The rectangle enclosure and point-dominance problems revisited, International Journal of Computational Geometry and Applications, 7 (5), 437-455, 1997.

  2. Prosenjit Gupta, Ravi Janardan, Michiel Smid and Bhaskar DasGupta, The rectangle enclosure and point-dominance problems revisited, 11th ACM Symposium on Computational Geometry, 162-171, 1995.

"Piecewise linear systems" (reverse chronological order)
  1. Bhaskar DasGupta and Eduardo D. Sontag, A Polynomial-Time Algorithm for Checking Equivalence Under Certain Semiring Congruences motivated by the State-space Isomorphism Problem for Hybrid Systems, Theoretical Computer Science, 262 (1), 161-189, 2001.

  2. Bhaskar DasGupta and Eduardo D. Sontag, A Polynomial-Time Algorithm for an Equivalence Problem which Arises in Hybrid Systems Theory, 37th IEEE Conference on Decision and Control, IEEE Publications, 1629-1634, 1998.

"Monotone systems" (reverse chronological order)
  1. Bhaskar DasGupta, German Andres Enciso, Eduardo Sontag and Yi Zhang, Algorithmic and Complexity Results for Decompositions of Biological Networks into Monotone Subsystems, Biosystems, 90 (1), 161-178, 2007.

  2. Bhaskar DasGupta, German Andres Enciso, Eduardo Sontag and Yi Zhang, Algorithmic and Complexity Results for Decompositions of Biological Networks into Monotone Subsystems, 5th International Workshop Experimental Algorithms (WEA), LNCS 4007, 253-264, Springer-Verlag, 2006.

"Honey-pot searching" (reverse chronological order)
  1. Bhaskar DasGupta, João P. Hespanha, James Riehl and Eduardo Sontag, Honey-pot Constrained Searching with Local Sensory Information , Journal of Nonlinear Analysis: Hybrid Systems and Applications , 65 (9), 1773-1793, 2006.

  2. Bhaskar DasGupta, João P. Hespanha and Eduardo Sontag, Computational Complexities of Honey-pot Searching with Local Sensory Information, 2004 American Control Conference (ACC 2004), 2134-2138, 2004.

  3. Bhaskar DasGupta, João P. Hespanha and Eduardo Sontag, Aggregation-based Approaches to Honey-pot Searching with Local Sensory Information, 2004 American Control Conference (ACC 2004), 1202-1207, 2004.

"Cover / multi-cover" (reverse chronological order)
  1. Mary V. Ashley, Tanya Y. Berger-Wolf, Wanpracha Chaovalitwongse, Bhaskar DasGupta, Ashfaq Khokhar and Saad Sheikh, On Approximating An Implicit Cover Problem in Wild Population Study, Discrete Mathematics, Algorithms and Applications, 2 (1), 21-31, 2010.

  2. Mary Ashley, Tanya Y. Berger-Wolf, Piotr Berman, Wanpracha Chaovalitwongse, Bhaskar DasGupta and Ming-Yang Kao, On Approximating Four Covering and Packing Problems , Journal of Computer and System Sciences, 75 (5), 287-302, 2009.

  3. Mary V. Ashley, Tanya Y. Berger-Wolf, Wanpracha Chaovalitwongse, Bhaskar DasGupta, Ashfaq Khokhar and Saad Sheikh, On Approximating An Implicit Cover Problem in Biology, 5th International Conference on Algorithmic Aspects in Information and Management (AAIM), A. Goldberg and Y. Zhou (Eds.), LNCS 5564, 43-54, ©Springer-Verlag Berlin Heidelberg, 2009.

  4. Piotr Berman and Bhaskar DasGupta, Approximating the Online Set Multicover Problems Via Randomized Winnowing, Theoretical Computer Science, 393 (1-3), 54-71, 2008.

  5. Mary Ashley, Tanya Berger-Wolf, Piotr Berman, Wanpracha Chaovalitwongse, Bhaskar DasGupta and Ming-Yang Kao, Approximating Several Covering/Packing Problems, International Symposium on Combinatorial Optimization 2008, University of Warwick, Coventry, UK, 2008 (abstract only).

  6. Piotr Berman, Bhaskar DasGupta and Eduardo Sontag, Randomized Approximation Algorithms for Set Multicover Problems with Applications to Reverse Engineering of Protein and Gene Networks, Discrete Applied Mathematics, 155 (6-7), 733-749, 2007.

  7. Piotr Berman and Bhaskar DasGupta, Approximating the Online Set Multicover Problems Via Randomized Winnowing, 9th Workshop on Algorithms and Data Structures (WADS), F. Dehne, A. Lòpez-Ortiz and J. R. Sack (editors), LNCS 3608, Springer-Verlag, 110-121, 2005.
                      (A complete version of the paper with all the proofs is here)

  8. Piotr Berman, Bhaskar DasGupta and Eduardo Sontag, Randomized Approximation Algorithms for Set Multicover Problems with Applications to Reverse Engineering of Protein and Gene Networks, 7th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems (APPROX), LNCS 3122, K. Jansen, S. Khanna, J. D. P. Rolim and D. Ron (eds.), Springer Verlag, 39-50, 2004.
                      (A revised journal version with somewhat improved bounds is available here)

  9. Bhaskar DasGupta, Ravi Janardan and Naveed Sherwani, On the Greedy Algorithm for a Covering Problem, Technical Report # TR 93-13, Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, February 1993.

"Transitive reduction" (reverse chronological order)
  1. Piotr Berman, Bhaskar DasGupta and Marek Karpinski, Approximating Transitive Reduction Problems for Directed Networks, 11th Algorithms and Data Structures Symposium (WADS), F. Dehne, M. Gavrilova, J.-R. Sack and C. D. Tóth (eds.), LNCS 5664, 74-85, 2009.

  2. Réka Albert, Bhaskar DasGupta, Riccardo Dondi and Eduardo Sontag, Inferring (Biological) Signal Transduction Networks via Transitive Reductions of Directed Graphs, Algorithmica, 51 (2), 129-159, 2008.

"Strong metric dimension" (reverse chronological order)
  1. Bhaskar DasGupta and Nasim Mobasheri, On optimal approximability results for computing the strong metric dimension, Discrete Applied Mathematics, 221, 18-24, 2017.

    Here are some pdf slides for these results (from the talk at the 8th Slovenian International Conference on Graph Theory, Kranjska Gora, Slovenia, 2015).


"Modularity maximization" (reverse chronological order)
  1. Bhaskar DasGupta and Devendra Desai, On a Connection Between Small Set Expansions and Modularity Clustering, Information Processing Letters, 114 (7), 349-352, 2014.

  2. Bhaskar DasGupta, Computational Complexities of Optimization Problems Related to Model Based Clustering of Networks, in Optimization in Science and Engineering - in Honor of the 60th Anniversary of Birth of Panos Pardalos, S. Butenko, C. Floudas and Th. M. Rassias (editors), 97-113, Springer, 2014.

  3. Bhaskar DasGupta and Devendra Desai, Complexity of Newman's Community Finding Approach for Social Networks, Journal of Computer and System Sciences, 79, 50-67, 2013.
                      (this paper was also be presented at the ICALP 2011 workshop on Graph algorithms and Applications, Zurich, Switzerland, July 3, 2011).

"Steiner trees and computer networks" (reverse chronological order)
  1. Xinzhen Cheng, Bhaskar DasGupta and Bing Lu, Polynomial Time Approximation Scheme for the Symmetric Rectilinear Steiner Arborescence Problem, Journal of Global Optimization, 21 (4), 385-396, 2001.

  2. Sourav Bhattacharya and Bhaskar DasGupta, Steiner Problem in Multistage Computer Networks, in D.-Z. Du and P. M. Pardalos (eds.), Network Optimization Problems, World Scientific Publishing Co., 387-401, 1993.

"Hypercube routing"
  1. Frank K. Hwang, Yi-Ching Yao and Bhaskar DasGupta, Some permutation routing algorithms for lower-dimensional hypercubes, Theoretical Computer Science, 270 (1-2), 111-124, 2002.

"Traffic networks" (reverse chronological order)
  1. Daniel Ayala, Ouri Wolfson, Bhaskar DasGupta, Jie Lin and Bo Xu, Spatio-temporal Matching for Urban Transportation Applications, ACM Transactions on Spatial Algorithms and Systems, 3(4), 11:1-11:39, 2018.

  2. Daniel Ayala, Ouri Wolfson, Bo Xu, Bhaskar Dasgupta and Jie Lin, Pricing of Parking for Congestion Reduction, 20th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems, 43-51, 2012.

  3. Daniel Ayala, Ouri Wolfson, Bo Xu, Bhaskar Dasgupta and Jie Lin, Spatio-temporal Matching Algorithms for Road Networks, 20th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems, 518-521, 2012.

  4. Daniel Ayala, Ouri Wolfson, Bo Xu, Bhaskar Dasgupta and Jie Lin, Stability of Marriage and Vehicular Parking, 2nd International Workshop on Matching Under Preferences, Budapest, Hungary, July 10-20, 2012.

  5. Daniel Ayala, Ouri Wolfson, Bo Xu, Bhaskar Dasgupta and Jie Lin, Parking in Competitive Settings: A Gravitational Approach, 13th International Conference on Mobile Data Management, IEEE Press, 27-31, 2012.

  6. Daniel Ayala, Ouri Wolfson, Bo Xu, Bhaskar Dasgupta and Jie Lin, Parking Slot Assignment Games, 19th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems, 299-308, 2011.

"Cuts and Expansions" (reverse chronological order)
  1. Bhaskar DasGupta, Marek Karpinski, Nasim Mobasheri and Farzane Yahyanejad, Effect of Gromov-hyperbolicity Parameter on Cuts and Expansions in Graphs and Some Algorithmic Implications, Algorithmica, 80(2), 772-800, 2018.

    Here are some pdf slides for these results (from the talk at BCTCS-2016).

  2. Bhaskar DasGupta and Devendra Desai, On a Connection Between Small Set Expansions and Modularity Clustering, Information Processing Letters, 114 (7), 349-352, 2014.

"Anomaly detection" (reverse chronological order)
  1. Bhaskar DasGupta, Mano Vikash Janardhanan and Farzane Yahyanejad, How did the shape of your network change? (On detecting network anomalies via non-local curvatures), arXiv:1808.05676 [cs.DS], 2018.

"Clustering" (reverse chronological order)
  1. Bhaskar DasGupta and Devendra Desai, On a Connection Between Small Set Expansions and Modularity Clustering, Information Processing Letters, 114 (7), 349-352, 2014.

  2. Bhaskar DasGupta, Computational Complexities of Optimization Problems Related to Model Based Clustering of Networks, in Optimization in Science and Engineering - in Honor of the 60th Anniversary of Birth of Panos Pardalos, S. Butenko, C. Floudas and Th. M. Rassias (editors), 97-113, Springer, 2014.

  3. Bhaskar DasGupta and Devendra Desai, Complexity of Newman's Community Finding Approach for Social Networks, Journal of Computer and System Sciences, 79, 50-67, 2013.
                      (this paper was also be presented at the ICALP 2011 workshop on Graph algorithms and Applications, Zurich, Switzerland, July 3, 2011).

  4. Piotr Berman, Bhaskar DasGupta, Ming-Yang Kao and Jie Wang, On Constructing An Optimal Consensus Clustering from Multiple Clusterings, Information Processing Letters, 104 (4), 137-145, 2007.

"Graph theory" (reverse chronological order)
  1. Gerard J. Chang, Bhaskar DasGupta, Wayne M. Dymàcek, Martin Fürer, Matthew Koerlin, Yueh-Shin Lee and Tom Whaley, Characterizations of Bipartite Steinhaus Graphs, Discrete Mathematics, 199 (1-3), 11-25, 1999.

  2. Bhaskar DasGupta and Martin Fürer, Counting Bipartite Steinhaus Graphs, 7th SIAM Conference on Discrete Mathematics, 1994 (abstract only).

"Boolean formula minimization"
  1. Amitabha Bhattacharya, Bhaskar DasGupta, Dhruv Mubayi and György Turàn, On Approximate Horn Formula Minimization, 37th International Colloquium on Automata, Languages and Programming (ICALP), S. Abramsky et al. (eds.), Part I, LNCS 6198, 438-450, © Springer-Verlag Berlin Heidelberg, 2010.

"Web integration" (reverse chronological order)
  1. Eduard C. Dragut, Brian P. Beirne, Bhaskar DasGupta, Ali Neyestani, Badr Atassi, Clement Yu and Weiyi Meng, Merging Query Results From Local Search Engines for Geo-referenced Objects, ACM Transactions on the Web, 8(4), 20:1-20:29, 2014.

  2. Eduard Dragut, Brian Beirne, Ali Neyestani, Badr Atassi, Clement Yu, Bhaskar DasGupta and Weiyi Meng, YumiInt --- A Deep Web Integration System for Local Search Engines for Geo-referenced Objects, 29th IEEE International Conference on Data Engineering, 1352-1355, 2013.
"Election gerrymandering" (reverse chronological order)
  1. Tanima Chatterjee and Bhaskar DasGupta, On partisan bias in redistricting: computational complexity meets the science of gerrymandering, arXiv:1910.01565, 2019.

  2. Tanima Chatterjee, Bhaskar DasGupta, Laura Palmieri, Zainab Al-Qurashi and Anastasios Sidiropoulos, Alleviating partisan gerrymandering: can math and computers help to eliminate wasted votes?, arXiv:1804.10577 [cs.CY], 2018.